[English] 日本語
Yorodumi
- PDB-3tvt: Structural basis for Discs Large interaction with Pins -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tvt
TitleStructural basis for Discs Large interaction with Pins
Components
  • Disks large 1 tumor suppressor protein
  • Partner of Inscuteable
KeywordsANTITUMOR PROTEIN/PROTEIN BINDING / Dlg / Src-homology-3 / Guanylate kinase / Phosphorylation-dependent / Cell membrane / ANTITUMOR PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


smooth septate junction / positive phototaxis / RHO GTPases activate CIT / Neurexins and neuroligins / establishment or maintenance of polarity of larval imaginal disc epithelium / negative regulation of imaginal disc growth / cell fate commitment involved in pattern specification / type I terminal bouton / septate junction / septate junction assembly ...smooth septate junction / positive phototaxis / RHO GTPases activate CIT / Neurexins and neuroligins / establishment or maintenance of polarity of larval imaginal disc epithelium / negative regulation of imaginal disc growth / cell fate commitment involved in pattern specification / type I terminal bouton / septate junction / septate junction assembly / G alpha (i) signalling events / Activation of Ca-permeable Kainate Receptor / morphogenesis of follicular epithelium / type Ib terminal bouton / subsynaptic reticulum / Synaptic adhesion-like molecules / establishment or maintenance of polarity of follicular epithelium / morphogenesis of larval imaginal disc epithelium / Unblocking of NMDA receptors, glutamate binding and activation / gravitaxis / tricellular tight junction / anterior/posterior axis specification, follicular epithelium / pole plasm protein localization / establishment of spindle orientation / negative regulation of peptidoglycan recognition protein signaling pathway / basal protein localization / asymmetric protein localization involved in cell fate determination / dorsal closure / follicle cell of egg chamber development / regulation of epidermal growth factor receptor signaling pathway / positive regulation of synaptic assembly at neuromuscular junction / male courtship behavior / asymmetric cell division / guanylate kinase activity / asymmetric neuroblast division / morphogenesis of a polarized epithelium / epithelial structure maintenance / receptor localization to synapse / behavioral response to ethanol / apical cortex / leading edge membrane / apicolateral plasma membrane / establishment or maintenance of epithelial cell apical/basal polarity / synaptic assembly at neuromuscular junction / GDP-dissociation inhibitor activity / mating behavior / cell fate specification / receptor clustering / locomotor rhythm / establishment of mitotic spindle orientation / regulation of postsynaptic membrane neurotransmitter receptor levels / lateral plasma membrane / neuroblast proliferation / G-protein alpha-subunit binding / postsynaptic density membrane / neuromuscular junction / terminal bouton / cell-cell adhesion / nervous system development / cell cortex / basolateral plasma membrane / chemical synaptic transmission / postsynaptic membrane / cytoskeleton / neuron projection / protein domain specific binding / synapse / protein kinase binding / perinuclear region of cytoplasm / signal transduction / membrane / plasma membrane
Similarity search - Function
: / GoLoco motif / L27-1 / GoLoco motif / L27_1 / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / domain in receptor targeting proteins Lin-2 and Lin-7 ...: / GoLoco motif / L27-1 / GoLoco motif / L27_1 / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Tetratricopeptide repeat / Disks large 1-like / : / Guanylate kinase, conserved site / Tetratricopeptide repeat / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / SH3 Domains / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tetratricopeptide-like helical domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Disks large 1 tumor suppressor protein / Partner of Inscuteable / LD33695p
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsJohnston, C.A. / Doe, C.Q. / Prehoda, K.E.
CitationJournal: To be Published
Title: Structural basis for Discs Large interaction with Pins
Authors: Johnston, C.A. / Doe, C.Q. / Prehoda, K.E.
History
DepositionSep 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Disks large 1 tumor suppressor protein
B: Partner of Inscuteable


Theoretical massNumber of molelcules
Total (without water)39,5862
Polymers39,5862
Non-polymers00
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-8 kcal/mol
Surface area14830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.604, 94.546, 83.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Disks large 1 tumor suppressor protein


Mass: 33849.078 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: dlg1, l(1)dlg1, CG1725 / Plasmid: pBH4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P31007
#2: Protein/peptide Partner of Inscuteable / Pins


Mass: 5737.344 Da / Num. of mol.: 1 / Fragment: linker domain (UNP residues 411-460) / Mutation: S436D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: raps, pins, CG5692 / Plasmid: pBH4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NH88, UniProt: Q9VB22*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDISCS LARGE FRAGMENT COMPRISES SH3 DOMAIN (UNP RESIDUES 618-698) AND GUANYLATE KINASE-LIKE DOMAIN ...DISCS LARGE FRAGMENT COMPRISES SH3 DOMAIN (UNP RESIDUES 618-698) AND GUANYLATE KINASE-LIKE DOMAIN (UNP RESIDUES 762-970) WITH RESIDUES 699-761 DELETED.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2M NaCl, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2009
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 47972 / Num. obs: 45138 / % possible obs: 94.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 6.9 % / Biso Wilson estimate: 23.74 Å2 / Rsym value: 0.04 / Net I/σ(I): 55.4
Reflection shellResolution: 1.6→1.66 Å / % possible all: 95.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→31.34 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.779 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.094 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24545 2400 5 %RANDOM
Rwork0.22016 ---
obs0.22141 45138 99.07 %-
all-47972 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2--0.25 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.6→31.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2200 0 0 234 2434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222247
X-RAY DIFFRACTIONr_angle_refined_deg1.7521.9563032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6615264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0623.451113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8315408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8811521
X-RAY DIFFRACTIONr_chiral_restr0.1150.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211707
X-RAY DIFFRACTIONr_mcbond_it1.1241.51341
X-RAY DIFFRACTIONr_mcangle_it2.03522178
X-RAY DIFFRACTIONr_scbond_it3.143906
X-RAY DIFFRACTIONr_scangle_it5.084.5854
LS refinement shellResolution: 1.6→1.644 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 153 -
Rwork0.316 3102 -
obs--93.19 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.05072.60030.52655.07822.29831.45350.2109-0.2725-0.12990.0328-0.3118-0.10480.0026-0.21770.10080.1126-0.0886-0.01450.1223-0.04390.108628.630924.1232-1.6018
21.41110.08480.80910.42580.0581.45750.00690.04110.0864-0.0449-0.0074-0.08090.04170.2080.00050.0297-0.00310.02160.0415-0.01090.041517.55044.2467-18.1065
36.15412.9281-0.62699.297-2.83093.82820.22480.1699-0.7343-0.2256-0.389-0.63340.25530.85070.16420.07970.0393-0.03360.25410.00980.120817.9085-0.028-30.4665
432.9062-21.9124-21.402117.86715.940517.31260.2683-0.55121.71690.27520.0103-0.0439-1.45760.0074-0.27860.9913-0.0108-0.0410.29880.00330.606813.925817.4902-28.1459
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A602 - 779
2X-RAY DIFFRACTION2A780 - 971
3X-RAY DIFFRACTION3B434 - 442
4X-RAY DIFFRACTION4B443 - 447

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more